Ph.D. - Computer Science
Permanent URI for this collection
Browse
Recent Submissions
Item HUMAN-CENTERED AI DEVELOPMENT FOR AUGMENTED COGNITION(2024) Doliashvili, Mariam; Crosby, Martha E.; Computer ScienceItem Follow-Up Questions Improve Generative AI Output and User Experience: Working Towards a Collaborative Model of Human-AI Interaction(2024) Tix, Bernadette Jzexoia; Binsted, Kim; Computer ScienceItem The Makawalu Visualization Environment: Defining Design Practice of Spatial Augmented Realities for Place-Based Learning in Indigenous Education(2024) Noe, Kari; Leigh, Jason; Computer ScienceItem TEXT SUMMARIZATION IN QUANTUM COMPUTING(2024) Mohamed, Muzamil; Crosby, Martha E.; Computer ScienceItem Model-agnostic Trajectory Abstraction and Visualization Method for Explainability in Reinforcement Learning(2024) Takagi, Yoshiki; Leigh, Jason; Computer ScienceItem Parallel Cache-Efficient Algorithms on GPUs(University of Hawaii at Manoa, 2023) Berney, Kyle Mitsuo; Sitchinava, Nodari S.; Computer ScienceGraphics Processing Units (GPUs) have emerged as a highly attractive architecture for general-purpose computing due to their numerous programmable cores, low-latency memory units, and efficient thread context switching capabilities. However, theoretical research on parallel algorithms for GPUs is challenging due to the multitude of interdependent factors influencing overall runtime. Computational models are commonly employed to provide simplified abstractions of computing system architectures. However, developing a computational model that is both simple and accurate, encompassing all performance-affecting aspects of GPU algorithms, is a seemingly impossible task. Existing GPU models often incorporate numerous variables to account for specific performance factors, rendering them less accessible to researchers. This dissertation obviates the lack of a widely accepted model of computation for GPUs by instead employing multiple classical parallel models to capture both parallel computational complexity and cache-efficiency. Namely, we leverage existing knowledge and algorithmic techniques from the Parallel Random Access Machine (PRAM), Parallel External Memory (PEM), and Distributed Memory Machine (DMM) models to aid in the design and analysis of GPU algorithms at various levels of detail. We validate and demonstrate our approach through case studies on specific problems (e.g., sorting, searching, and single source shortest paths), providing both theoretical analysis and corresponding empirical results. Our results highlights the applicability of the selected parallel models of computation to GPUs and illustrates how theoretical research can expose valuable insights into the performance of GPU algorithms in practice.Item Novel algorithms to account for uncertainties in the sequencing of genetic material with skewed abundance(University of Hawaii at Manoa, 2022) Arisdakessian, Cedric; Belcaid, Mahdi; Poisson, Guylaine; Computer ScienceThe sequencing of genetic material (microbial DNA or RNA) is essential in biological experiments. However, while the cost of sequencing has decreased substantially, the highly skewed distribution of genetic material makes it challenging to accurately represent the genetic content of a sample. For instance, in DNA-based metagenomic experiments, DNA fragments are randomly sampled and used to identify and quantify organisms present in an environmental sample. Rare species are sampled less frequently, thus challenging subsequent bioinformatic analyses. Given the prevalence and the drastic implications of the uneven distribution of genetic material on bioinformatic analyses, our research focuses on new graph- and deep learning-based methods to address these issues in three different contexts. Specifically, we propose (1) an imputation method that can accurately recover the abundance of under-represented genetic material in single-cell RNA-seq experiments (2) a binning method to reduce genome fragmentation in viral metagenome sequencing experiments, and (3) a tool to explore and cluster viral populations based on their genomic structure. Our contributions focus on three popular biological contexts for which the issue of abundance hampers the bioinformatic analyses. Furthermore, the last two chapters focus on understanding viral diversity and modeling the genesis of novel virus strains through recombinations. Despite being at the core of the current COVID-19 crisis, the issue of recombination remains understudied, and few tools exist to model how viral populations evolve through recombination.Item Decentralized Multi-robot SLAM And Ad Hoc Network For Exploration In A Remote And Enclosed Environment(University of Hawaii at Manoa, 2022) Idota, Tetsuya; Baek, Kyungim; Computer ScienceRobotic exploration in an enclosed, unknown, and unstructured environment such as a cave is a challenging problem as the robots cannot directly communicate with any exterior facilities. In such an environment, the robots need to perform Simultaneous Localization and Mapping (SLAM) without any external supports, e.g., GPS, a prior map, wifi access points, and so on. To cope with this situation, the proposed method establishes a decentralized multi-robot system forming an ad hoc network. Each robot is deployed at the entrance of the environment and moves into deeper areas while maintaining the distances to its neighboring robots to locally communicate with each other. In this formation, they perform the decentralized cooperative localization and the distributed submap building. The decentralized cooperative localization enables the robots to localize themselves with respect to the global reference frame by taking mutual measurements on a relative pose between the robots. Communicating with neighboring robots, each robot updates its estimated location based on sensory data about relative poses with respect to the neighbors and their estimated locations. To deal with the overconfidence problem, which leads to inconsistent estimates due to cyclic updates, the proposed method performs the conservative data exchange. When the robots pass their estimation to each other, they reduce the confidence in their estimation by applying fractional exponents to the probability distributions. As a result, the distributions become "smoother" with less intense peaks. Thereby, the robots can avoid inconsistent amplification of confidence and update their estimation based on each other's information without the knowledge about the entire network topology. The distributed submap building directs the robots to cooperatively build submaps, each of which represents a small local area in the environment. Each robot builds a series of submaps along its trajectory. When the robot detects that its neighboring robots enter the areas where submaps were built previously and can no longer update the submaps by itself, it passes the submaps to such robots so that the submaps can be used by the receiving robots. Thus, each of the robots does not have to hold all the submaps that it has created from the beginning of the operation, and hence can save the memory space for the mapping process. Consequently, the robots can deliver consistent results of mapping and localization in a decentralized manner while holding only the submaps associated with their local areas. The proposed methods are implemented in Robot Operating System (ROS) and the protocols for the communication are also designed. For experiments, demonstration, and evaluation, the implemented system is simulated using the Gazebo simulator.Item Research through Design of Bendable Interactive Playing Cards(University of Hawaii at Manoa, 2021) Kirshenbaum, Nurit; Robertson, Scott P.; Computer ScienceComputer Interaction has become second nature for almost all modern people and touch interaction on smart devices has likewise become ubiquitous. It is easy to forget how new the touch interaction paradigms are and the path it took to develop them. Nowadays, interaction designers are looking for even more novel interaction techniques with previously unheard of input and output channels. One direction for this search is bendable interfaces - interfaces that require their users to bend them as a form of interaction. In this work, I will overview and analyze a collection of prior academic research relating to bendable devices. Researchers often wonder: what will work well with bend interactions? In this dissertation I offer the answer "bendable interactive playing cards", and I frame my work on this word-salad using the Research through Design methodology. Ultimately, I hope to answer the question: Is bending interaction suitable, feasible, and expressive for interactive playing cards? My interactive playing card devices, which I call PEPA (Paper-like Entertainment Platform Agents) are inspired by my love of both paper-based and digital card games. By combining computational capabilities in multiple stand-alone physical devices, I can offer more than the two media forms can offer separately. I describe 6 possible scenarios where such a system can be used as well as other hybrid digital-physical game systems inspired by card and board games. Of course, the concept of interactive playing cards does not automatically lend itself to bend interaction, so I will try to justify this integration of ideas via a study of the literature and my observations of card players. Following my arguments to incorporate bending and interactive cards, I created a proof-of-concept prototype. In true Research through Design form, this was a situation where one has to build an object before they can understand what research directions to take. In this case, the prototype led to further user studies regarding the timing of actions during the bend gesture and a model for bend events. At a different point, I used design as a research activity when I conducted a workshop for designing games for interactive cards. I will report the procedure, results and analysis from this workshop to illustrate the design space of possible games. Research through Design is a research approach within the field of HCI that has multiple, sometimes conflicting, interpretations. It is mostly agreed that such research involves the creation of some prototype and an end goal of extracting and disseminating knowledge. In this work I will present the different approaches for documenting RtD as well as my own contribution: the Designer's Reframe and Refine Diagram. This is a method that uses a diagram as a tool to reflect on the design process as a whole in a prototype-centric way. I will show how I use this method to systematically document 5 versions of prototype in the PEPA project.Item SageXR - Design, Development And Study Of Efficacy And User Behavior In Virtual And Augmented Reality Project Rooms(University of Hawaii at Manoa, 2021) Kobayashi, Dylan; Leigh, Jason; Computer ScienceRecent years have seen a decrease in cost with significant improvements in quality of XR (Augmented and Virtual Reality) headsets. XR devices are no longer limited to research facilities and have made their way into the consumer market where they are known for entertainment. Over the decades, research has shown the immersion provided by XR devices improves user memory and performance, where its nature is especially suited to 3D and multidimensional data. XR devices are traditionally used in a support role to provide a focused experience or as an inspection apparatus; similar to the role of a microscope. But, such a role prevents XR devices from supporting information analysis from start to finish. Part of this is related to the bias towards 3D and often exclusion of 2D applications which are common in our daily work. However, XR devices have great potential for supporting project room usage of ideation, brainstorming, and information analysis from start to finish. This thesis conducted research to answer hypotheses made in regards to working within immersive environments. The contributions are: COVACh, a framework to guide the design of a system based on user interaction states with information media; SageXR a working prototype designed using the framework; and the discoveries made while testing SageXR to verify the hypothesis. COVACh was found to be successful in guiding the design of SageXR; all user study participants were able to submit their task work for evaluation and formed a favorable option regarding XR’s potential to support project room usage. All participants were observed to make use of at least 2x more virtual area than physical area by the end of their task work, indicating that provided the opportunity, participants wanted and were able to incorporate more space into their workflow than physically accessible. Participants not only used more space but also created information structures which, in some cases, would not be physically possible to replicate due to accessibility. Interestingly there seems to be an underlying desire for layout support best described as dynamic tiled display wall structures within the virtual environment. These are just some of the discoveries made which also includes some caveats found during usage of SageXR. Discussion regarding future development directions and how to address these caveats are covered, describing how SageXR can support usage beyond the project room.